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Fluorine in PDB 6hf0: M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.

Enzymatic activity of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.

All present enzymatic activity of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.:
1.1.98.3;

Protein crystallography data

The structure of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone., PDB code: 6hf0 was solved by K.Futterer, S.M.Batt, G.S.Besra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.29 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.640, 85.410, 80.410, 90.00, 103.20, 90.00
R / Rfree (%) 21.2 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. (pdb code 6hf0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone., PDB code: 6hf0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 1 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:68.0
occ:1.00
 F28 A:G1H901 0.0 68.0 1.0
C7 A:G1H901 1.3 68.2 1.0
F29 A:G1H901 2.1 64.0 1.0
F27 A:G1H901 2.2 69.2 1.0
C6 A:G1H901 2.3 68.3 1.0
C5 A:G1H901 2.9 61.0 1.0
C A:GLY133 3.2 50.3 1.0
CD2 A:HIS132 3.3 53.9 1.0
O A:GLY133 3.3 46.3 1.0
C1 A:G1H901 3.5 62.8 1.0
CA A:GLY133 3.5 49.3 1.0
N A:LYS134 3.7 56.7 1.0
NE2 A:HIS132 4.0 51.0 1.0
CD A:LYS367 4.0 54.5 1.0
N A:GLY133 4.1 48.0 1.0
C4 A:G1H901 4.2 71.3 1.0
CA A:LYS134 4.2 56.6 1.0
CG A:HIS132 4.4 45.9 1.0
O4 A:FAD900 4.5 47.2 1.0
C A:HIS132 4.5 41.0 1.0
O A:HIS132 4.6 42.0 1.0
C2 A:G1H901 4.6 70.3 1.0
CE1 A:PHE369 4.7 45.2 1.0
C3 A:G1H901 4.9 65.8 1.0
CG A:LYS134 4.9 66.8 1.0

Fluorine binding site 2 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 2 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:69.2
occ:1.00
 F27 A:G1H901 0.0 69.2 1.0
C7 A:G1H901 1.3 68.2 1.0
F29 A:G1H901 2.2 64.0 1.0
F28 A:G1H901 2.2 68.0 1.0
C6 A:G1H901 2.3 68.3 1.0
C1 A:G1H901 2.7 62.8 1.0
ND2 A:ASN385 3.1 55.0 1.0
C5 A:G1H901 3.6 61.0 1.0
CD2 A:HIS132 3.7 53.9 1.0
NE2 A:HIS132 3.8 51.0 1.0
CD A:LYS367 3.8 54.5 1.0
CE1 A:PHE369 3.9 45.2 1.0
CB A:LYS367 3.9 55.5 1.0
CG A:ASN385 4.0 51.3 1.0
C2 A:G1H901 4.1 70.3 1.0
CG A:LYS367 4.3 49.4 1.0
CZ A:PHE369 4.3 43.0 1.0
NE2 A:GLN336 4.6 46.8 1.0
OD1 A:ASN385 4.7 50.6 1.0
C4 A:G1H901 4.7 71.3 1.0
CB A:ASN385 4.8 45.0 1.0
SG A:CYS387 4.9 70.4 1.0
CD1 A:PHE369 4.9 48.7 1.0
C3 A:G1H901 4.9 65.8 1.0
O A:GLY133 4.9 46.3 1.0
CG A:HIS132 4.9 45.9 1.0
N8 A:G1H901 5.0 79.8 1.0
CG1 A:VAL365 5.0 56.0 1.0

Fluorine binding site 3 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 3 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:64.0
occ:1.00
 F29 A:G1H901 0.0 64.0 1.0
C7 A:G1H901 1.3 68.2 1.0
F28 A:G1H901 2.1 68.0 1.0
F27 A:G1H901 2.2 69.2 1.0
C6 A:G1H901 2.3 68.3 1.0
C5 A:G1H901 2.9 61.0 1.0
C1 A:G1H901 3.3 62.8 1.0
CD A:LYS367 3.4 54.5 1.0
CB A:LYS367 3.6 55.5 1.0
CG A:LYS367 4.0 49.4 1.0
CB A:SER228 4.0 58.2 1.0
CG1 A:VAL365 4.1 56.0 1.0
C4 A:G1H901 4.2 71.3 1.0
CA A:LYS134 4.3 56.6 1.0
CG A:LYS134 4.4 66.8 1.0
O A:GLY133 4.5 46.3 1.0
N A:LYS134 4.5 56.7 1.0
C A:GLY133 4.5 50.3 1.0
C2 A:G1H901 4.5 70.3 1.0
CE A:LYS367 4.7 48.9 1.0
O A:SER227 4.7 48.9 1.0
C3 A:G1H901 4.8 65.8 1.0
ND2 A:ASN385 4.9 55.0 1.0
CB A:LYS134 4.9 57.1 1.0
CA A:SER228 4.9 56.2 1.0
O A:PHE366 4.9 56.8 1.0
CA A:LYS367 5.0 52.8 1.0

Fluorine binding site 4 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 4 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:65.3
occ:1.00
 F28 B:G1H901 0.0 65.3 1.0
C7 B:G1H901 1.3 73.7 1.0
F29 B:G1H901 2.1 72.3 1.0
F27 B:G1H901 2.2 72.0 1.0
C6 B:G1H901 2.3 75.9 1.0
C5 B:G1H901 2.9 75.8 1.0
C B:GLY133 3.3 51.5 1.0
O B:GLY133 3.4 47.6 1.0
CD2 B:HIS132 3.4 56.5 1.0
C1 B:G1H901 3.4 61.0 1.0
CA B:GLY133 3.7 49.2 1.0
N B:LYS134 3.7 56.3 1.0
CD B:LYS367 4.0 53.6 1.0
NE2 B:HIS132 4.0 54.1 1.0
N B:GLY133 4.2 47.5 1.0
CA B:LYS134 4.2 53.8 1.0
C4 B:G1H901 4.2 84.7 1.0
CG B:HIS132 4.5 50.7 1.0
O4 B:FAD900 4.5 52.8 1.0
C2 B:G1H901 4.6 74.1 1.0
C B:HIS132 4.6 46.3 1.0
O B:HIS132 4.6 46.2 1.0
CE1 B:PHE369 4.7 48.8 1.0
CG B:LYS134 4.9 67.9 1.0
C3 B:G1H901 4.9 80.3 1.0
CE B:LYS367 5.0 46.2 1.0
CB B:LYS367 5.0 55.8 1.0

Fluorine binding site 5 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 5 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:72.0
occ:1.00
 F27 B:G1H901 0.0 72.0 1.0
C7 B:G1H901 1.3 73.7 1.0
F29 B:G1H901 2.2 72.3 1.0
F28 B:G1H901 2.2 65.3 1.0
C6 B:G1H901 2.3 75.9 1.0
C1 B:G1H901 2.7 61.0 1.0
ND2 B:ASN385 3.1 58.2 1.0
C5 B:G1H901 3.6 75.8 1.0
CB B:LYS367 3.8 55.8 1.0
CD B:LYS367 3.8 53.6 1.0
CD2 B:HIS132 3.9 56.5 1.0
CE1 B:PHE369 4.0 48.8 1.0
NE2 B:HIS132 4.0 54.1 1.0
CG B:ASN385 4.1 55.1 1.0
C2 B:G1H901 4.1 74.1 1.0
CG B:LYS367 4.2 46.7 1.0
CZ B:PHE369 4.5 42.9 1.0
C4 B:G1H901 4.7 84.7 1.0
NE2 B:GLN336 4.7 50.1 1.0
CB B:ASN385 4.8 51.9 1.0
OD1 B:ASN385 4.8 57.6 1.0
SG B:CYS387 4.8 78.1 1.0
CG1 B:VAL365 4.8 57.9 1.0
C3 B:G1H901 4.9 80.3 1.0
N8 B:G1H901 5.0 87.0 1.0
O B:GLY133 5.0 47.6 1.0

Fluorine binding site 6 out of 6 in 6hf0

Go back to Fluorine Binding Sites List in 6hf0
Fluorine binding site 6 out of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:72.3
occ:1.00
 F29 B:G1H901 0.0 72.3 1.0
C7 B:G1H901 1.3 73.7 1.0
F28 B:G1H901 2.1 65.3 1.0
F27 B:G1H901 2.2 72.0 1.0
C6 B:G1H901 2.3 75.9 1.0
C5 B:G1H901 2.9 75.8 1.0
CD B:LYS367 3.4 53.6 1.0
C1 B:G1H901 3.4 61.0 1.0
CB B:LYS367 3.6 55.8 1.0
CB B:SER228 3.9 58.9 1.0
CG1 B:VAL365 4.1 57.9 1.0
CG B:LYS367 4.1 46.7 1.0
CA B:LYS134 4.2 53.8 1.0
CG B:LYS134 4.2 67.9 1.0
C4 B:G1H901 4.2 84.7 1.0
N B:LYS134 4.5 56.3 1.0
O B:GLY133 4.5 47.6 1.0
C B:GLY133 4.5 51.5 1.0
O B:SER227 4.6 54.4 1.0
C2 B:G1H901 4.6 74.1 1.0
CE B:LYS367 4.7 46.2 1.0
CA B:SER228 4.8 57.5 1.0
CB B:LYS134 4.8 57.9 1.0
OG B:SER228 4.9 69.5 1.0
C3 B:G1H901 4.9 80.3 1.0
O B:PHE366 5.0 58.5 1.0
ND2 B:ASN385 5.0 58.2 1.0
CA B:LYS367 5.0 53.9 1.0

Reference:

A.Richter, I.Rudolph, U.Mollmann, K.Voigt, C.W.Chung, O.M.P.Singh, M.Rees, A.Mendoza-Losana, R.Bates, L.Ballell, S.Batt, N.Veerapen, K.Futterer, G.Besra, P.Imming, A.Argyrou. Novel Insight Into the Reaction of Nitro, Nitroso and Hydroxylamino Benzothiazinones and of Benzoxacinones with Mycobacterium Tuberculosis DPRE1. Sci Rep V. 8 13473 2018.
ISSN: ESSN 2045-2322
PubMed: 30194385
DOI: 10.1038/S41598-018-31316-6
Page generated: Thu Aug 1 21:06:19 2024

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